State regulators are about to consider forcing Sacramento to do a better job of cleaning up what it flushes into one of California’s most endangered ecosystems and important drinking water sources, the Delta.

Among the requirements under consideration are high-tech filters, biological systems to remove ammonia and other upgrades.

The Sacramento Regional County Sanitation District, which says the improvements will cost $2 billion, contends it should not have to spend so much for what it says are questionable benefits. The bigger problem, it says, is the amount of water pumped out of the Delta.

But scientists, environmentalists and big water agencies that have seen their supplies shrivel as the Delta’s environmental problems have grown are urging regulators to require better treatment at the Delta’s largest sewer system.

“For the ecosystem to be fixed, it’s got to be more than focusing on flows and pumping,” said Laura King Moon, assistant general manager for State Water Contractors, an association of water agencies that rely on Delta pumps.

“We’re the only ones that are bearing the burdens of fixing the ecosystem,” she said.

Sacramento’s ammonium discharges are reducing the amount of small food organisms from the Sacramento River to Suisun Bay, scientists say.

Sixty percent of the municipal wastewater dumped into the Delta comes from the Sacramento plant, which is the only major sewage treatment plant in the Delta that has not installed — or is not installing — an advanced sewage treatment system. The exceptions include a much smaller plant in Discovery Bay and one of two plants in Rio Vista.

Sacramento is the source of nearly all of the ammonia in the Delta, regulators say.

In the past, regulators figured that so much fresh water flows down the Sacramento — California’s largest river — that it would dilute the sewage discharges.

But the Delta’s ecosystem is in severe decline and researchers are increasingly pointing at ammonia and its chemical sister, ammonium, as culprits that may be reducing the amount of food for fish.

“There has been a lot of research in the last few years on ammonia,” said Ken Landau, assistant executive officer for the Central Valley Regional Water Quality Control Board, which is writing the sewage treatment plant’s new permit. “It is not killing the big fish but it is inhibiting the growth of algae and part of the food chain.”

A draft permit would require the agency to install filters to reduce giardia and cryptosporidium, protozoans that can cause intestinal illnesses, and cut ammonia discharges from 14 tons a day to 1 ton a day.

Sacramento officials say they will have to replace chlorine-based disinfection with ultraviolet treatments to meet the conditions in the new permit.

The district’s top manager said the improvement costs would boost the average residential sewer bill from about $40 per month to $80.

“We simply don’t think it’s a reasonable balance,” said Stan Dean, district engineer for the sewer agency. “The gains in the water quality and the Delta ecosystem are largely speculative.”

“Admittedly it’s a judgment,” Dean added. “If you are not a ratepayer, you’re certainly entitled to a different opinion. ” If money is no object, we should do everything. But, unfortunately, we don’t have infinite money in our society.”

For big water agencies around the state, the desire to see Sacramento better treat its wastewater comes from the hope that it will improve environmental conditions in the Delta enough to ease restrictions on water allocations.

The sewer plant has long been a concern for the Contra Costa Water District because of its effect on the water it supplies to some 550,000 Contra Costa residents.

Three years ago, the Concord-based district won a lawsuit — now being appealed — in which it said the Sacramento district did not adequately consider how Sacramento’s expansion plans would affect water quality around Contra Costa and other water intakes.

The other water districts often repeat the mantra that they are not to blame for the environmental problems that led to new restrictions on their ability to pump Delta water.

Look at the “other stressors,” they say, pointing to invader fish species, the diminished food supply for fish and unregulated water withdrawals.

But Sacramento’s treated sewage discharge tops their lists.

There is even a public-relations campaign called, “The Great Delta Toilet Bowl” to call attention to flushing into the Delta.

Sacramento officials responded with their own public relations drive, even commissioning a report early this year to demonstrate just how many fish the Delta pumps kill.

Scientists say the correct answer is “C,” all of the above.

“Science supports the concept that there are multiple stressors affecting the Delta ecosystem but science also shows that the current nutrient loading (especially total ammonia) may be one of the most important of those stressors,” wrote Cliff Dahm, lead scientist for the state’s Delta science program.

The issues will be addressed at a hearing Thursday at 11020 Sun Center Dr., Suite 200 in Rancho Cordova.

As of last week, the Central Valley Regional Water Quality Control Board’s governing board lacked a quorum due to vacancies. A spokesman for Gov. Arnold Schwarzenegger, Matt Connelly, said the governor’s office had a goal of maintaining a quorum on all state panels but he could not say when appointments might be made.

Landau, the regional board’s assistant executive officer, said that the hearing would take place in any case and if the board lacks a quorum the board members who are there would make a recommendation for the board to vote on once it has a sufficient number of members.

If a quorum is present, the board could approve or reject the draft permit, or modify it.